[Debian-med-packaging] Bug#897109: fastqc: autopkgtest fails with new version while succeeded in the past; htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed

[Paul Gevers]

Source: fastqc
Version: 0.11.7+dfsg-1
Severity: normal
User: debian-ci at lists.debian.org
Usertags: regression

With the upload of version 0.11.7+dfsg-1 of fastqc, the autopkgtest¹
started to fail with the error copied below. As I have zero experience
with java, I don't know what to make of this error. Could you please
investigate?

Paul

¹ https://ci.debian.net/packages/f/fastqc/unstable/amd64/autopkgtest

[14:03:24]: test run-unit-test: [-----------------------
Started analysis of example.fastq
Analysis complete for example.fastq
Archive:  example_fastqc.zip
   creating: example_fastqc/
   creating: example_fastqc/Icons/
   creating: example_fastqc/Images/
  inflating: example_fastqc/Icons/fastqc_icon.png
  inflating: example_fastqc/Icons/warning.png
  inflating: example_fastqc/Icons/error.png
  inflating: example_fastqc/Icons/tick.png
  inflating: example_fastqc/summary.txt
  inflating: example_fastqc/Images/per_base_quality.png
  inflating: example_fastqc/Images/per_tile_quality.png
  inflating: example_fastqc/Images/per_sequence_quality.png
  inflating: example_fastqc/Images/per_base_sequence_content.png
  inflating: example_fastqc/Images/per_sequence_gc_content.png
  inflating: example_fastqc/Images/per_base_n_content.png
  inflating: example_fastqc/Images/sequence_length_distribution.png
  inflating: example_fastqc/Images/duplication_levels.png
  inflating: example_fastqc/Images/adapter_content.png
  inflating: example_fastqc/fastqc_report.html
  inflating: example_fastqc/fastqc_data.txt
  inflating: example_fastqc/fastqc.fo
PASS	Basic Statistics	example.fastq
WARN	Per base sequence quality	example.fastq
PASS	Per tile sequence quality	example.fastq
PASS	Per sequence quality scores	example.fastq
WARN	Per base sequence content	example.fastq
WARN	Per sequence GC content	example.fastq
PASS	Per base N content	example.fastq
PASS	Sequence Length Distribution	example.fastq
PASS	Sequence Duplication Levels	example.fastq
WARN	Overrepresented sequences	example.fastq
PASS	Adapter Content	example.fastq
Failed to process toy.sam
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
	at
htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:373)
	at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:64)
	at
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100)
	at
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
	at
uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152)
	at
uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Caused by: java.io.IOException: Stream closed
	at
java.base/java.io.BufferedInputStream.getInIfOpen(BufferedInputStream.java:159)
	at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
	at
java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
	at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at
htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:436)
	at
htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(BlockCompressedInputStream.java:351)
	at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:51)
	at
htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:313)
	... 6 more
autopkgtest [14:03:29]: test run-unit-test: -----------------------]

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